Retinal (vitamin A aldehyde) is a chromophore that binds integral membrane proteins (opsins) to form light-absorbing pigments called rhodopsins. Rhodopsins are currently known to belong to two distinct protein families. The visual rhodopsins, found in the eye throughout the animal kingdom, are photosensory pigments. Archaeal rhodopsins, found in extreme halophilic environments, function as light-driven protons pumps (bacteriorhodopsins), chloride ion pumps (halorhodopsins), or photosensory receptors (sensory rhodopsins). The two protein families show no significant sequence similarity and may have different origins. They do, however, share identical topologies characterized by seven transmembrane α-helices that form a pocket in which retinal is covalently linked, as a pronated Schiff base (helix G).
The archaeal rhodopsins are able to generate a photocycle which produces a chemiosmotic membrane potential in response to light, as such light energy is converted into biochemical energy. Recently, a protein with high sequence similarity to the archaeal rhodopsins has also been retrieved in the eukaryote Neurospora crassa (J. A. Bieszke et al., Proceedings of National Academy of Sciences USA 96:8034, 1999). The eucaryal rhodopsin formed a photochemically reactive pigment when bound to all-trans retinal and exhibited photocycle kinetics similar to those of archaeal sensory rhodopsins (J. A. Bieszke et al., Biochemistry 38:14138, 1999). To date, however, no rhodopsin-like sequences have been reported in members of the domain Bacteria, and no light-driven proton pumps based on rhodopsin have ever before been functionally expressed in E coli. 
The phototropic conversion of light energy into biochemical energy using bacteriorhodopsin can be harnessed for a variety of processes and applications, such as bio-electronic applications and bio-materials, as has been reported in U.S. Pat. No. 5,757,525 for optical devices, U.S. Pat. No. 5,854,710 for optical Fourier processing, and U.S. Pat. No. 5,470,690 for optical information storage. Bacteriorhodopsin in bio-electronic applications is aimed to interface, integrate, or substitute the silicon based microelectronics systems as well as molecular devices. Bacteriorhodopsin as a bio-material is integrated, for instance, in optical films for light mediated computer memory applications and pattern recognition.
Previously, archaeal rhodopsins capable of generating a chemiosmotic membrane potential in response to light had only been found in halophilic archaea. Therefore, rhodopsins that originate from archaea adapted to highly saline environments cannot be functionally expressed in E. coli. Finally, the isolation and cultivation of halorhodopsins is an elaborate process. At present one does not foresee an economic utilization possible for this process (e.g. U.S. Pat. No. 5,290,699).
Accordingly, as one skilled in the art might readily acknowledge, there is a strong need to retrieve and provide rhodopsin-like sequences from naturally occurring members of the domain Bacteria.